Yosemite FileVault resizes application reopened windows after login

HI,
I have a weird behaviour of reopened application windows (Reopen windows when logging back in feature) after I switched on the FileVault disk encryption. I think that it could be due to the fact that login screen is in 1280x800 resolution and my set resolution is 1680x1050. FileVault has different login process, when I had it switched off I did not notice this issue.
Now when I log into the system I can see all application windows at the top left corner with the smaller screen size than the ones which have been when I shut down the computer.
I have MacBook PRO 2013 Retina, Yosemite OS X 10.10 (14A389)
Does anybody have the same issue?
Thanks a lot
Jiri

I am just seeing if anyone has a suggestion. The scenario is oddly similar. I had 2 drive in. First drive was being copied to second drive with Carbon Copy Cloner. First drive had some bad sectors and performance issues. Second drive wouldn't start up the system reliably, but the data was there. Installed a new drive, installed OS X 10.10.1. Everything runs great if I leave it there. Once I migrate the data from the 2nd drive in place, the loginwindow process slowly creeps up until 300 copies are running along with over 60 SecurityAgents. All memory is being used and the system is a challenge to work with (virtually impossible).
I am assuming a corrupt file is getting copied during the transfer, but I have no way to know what that file is. If it makes a difference, all loginwindow processes except "loginwindow console" are owned by root. "loginwindow console" is owned by my account as expected.

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